Re: [Samtools-help] Regarding consensus file

[Petr D. <pd...@sa...>]

Hi,

I don't see anything obviously wrong in your commands. Take a look in
calls.vcf.gz, are there any variants? 

Here is a brief documentation, maybe it will give some useful pointers
http://samtools.github.io/bcftools/howtos/consensus-sequence.html
http://samtools.github.io/bcftools/howtos/variant-calling.html

Best wishes,
Petr




On Tue, 2019-02-12 at 05:09 +0530, Renuka Agarwal wrote:
> Hi
> I am using samtools and bcftools to generate consensus sequences for
> my microbiome data. After generating sorted bam file from samtools, I
> used mpileup command of bcftools.
> Commands were
> bcftools mpileup -Ou -f reference.fa alignments.bam | bcftools call
> -mv -Oz -o calls.vcf.gz
> bcftools index calls.vcf.gz
> Then for making consensus I used
> bcftools consensus -f reference.fa calls.vcf.gz > consensus.fa
> But the file that is being produced is actually my database file,
> i.e., reference.fa= consensus.fa
> Can anyone help why is it happening and what is sample file (-s), how
> can i get that.
> Thank you!
> 
> Regards
> Renuka Agarwal
> PhD Scholar
> IISER Mohali
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